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- PDB-3dj9: Crystal Structure of an isolated, unglycosylated antibody CH2 domain -

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Basic information

Entry
Database: PDB / ID: 3dj9
TitleCrystal Structure of an isolated, unglycosylated antibody CH2 domain
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin / CH2 domain / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Secreted
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPrabakaran, P. / Vu, B.K. / Gan, J. / Dimitrov, D.S. / Ji, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of an isolated unglycosylated antibody C(H)2 domain.
Authors: Prabakaran, P. / Vu, B.K. / Gan, J. / Feng, Y. / Dimitrov, D.S. / Ji, X.
History
DepositionJun 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 1, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)12,0881
Polymers12,0881
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.144, 40.678, 39.131
Angle α, β, γ (deg.)90.00, 106.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 12087.820 Da / Num. of mol.: 1 / Fragment: CH2 constant domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P01857
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 30% PEG 1500, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Aug 23, 2006 / Details: Mirror
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 11044 / Num. obs: 11044 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 5.4 / Num. unique all: 11044 / % possible all: 57.8

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Processing

Software
NameVersionClassification
PHENIXPHENIX.REFINErefinement
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZH

1hzh


Resolution: 1.75→26.361 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / σ(F): 0.17 / Phase error: 23.46 / Stereochemistry target values: ML
Details: THE REFINEMENT WAS DONE MAINLY WITH CNS 1.1 AND FINISHED WITH PHENIX
RfactorNum. reflection% reflection
Rfree0.227 542 5.17 %
Rwork0.201 9951 -
obs0.203 10493 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.717 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 47.39 Å2 / Biso mean: 22.847 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.409 Å2-0 Å21.156 Å2
2---3.707 Å2-0 Å2
3---8.116 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→26.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 111 962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007883
X-RAY DIFFRACTIONf_angle_d1.461191
X-RAY DIFFRACTIONf_chiral_restr0.09137
X-RAY DIFFRACTIONf_plane_restr0.008148
X-RAY DIFFRACTIONf_dihedral_angle_d19.712325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.820.311450.23684789272
1.82-1.9030.228520.2271007105987
1.903-2.0030.206610.2071133119497
2.003-2.1290.289600.2081135119598
2.129-2.2930.244580.2051138119698
2.293-2.5240.27750.231151122699
2.524-2.8890.27550.2371171122699
2.889-3.6380.22720.18911661238100
3.638-26.3640.161640.16612031267100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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